Known Issues
Package List
ADGofTest-0.3 Anderson-Darling GoF testALDEx2-1.34.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountALL-1.44.0 A data packageAgiMicroRna-2.52.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAnnotationDbi-1.64.1 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.26.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.44.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.10.0 Client to access AnnotationHub resourcesArchR 1.0.2 [CRAN]
BDgraph-2.72 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.84.0-0 Boost C++ Header FilesBSgenome-1.70.2 Software infrastructure for efficient representation of full genomes and their SNPsBSgenome.Hsapiens.UCSC.hg19-1.4.3 Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)Bhat-0.9-12 General Likelihood ExplorationBiasedUrn-2.0.11 Biased Urn Model DistributionsBiobase-2.62.0 Biobase: Base functions for BioconductorBiocBaseUtils-1.4.0 General utility functions for developing Bioconductor packagesBiocFileCache-2.10.2 Manage Files Across SessionsBiocGenerics-0.48.1 S4 generic functions used in BioconductorBiocIO-1.12.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.22 Access the Bioconductor Project Package RepositoryBiocNeighbors-1.20.2 Nearest Neighbor Detection for Bioconductor PackagesBiocParallel-1.36.0 Bioconductor facilities for parallel evaluationBiocSingular-1.18.0 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.30.0 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.18.1 Set the appropriate version of Bioconductor packagesBiostrings-2.70.3 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2-41 Functions for Elementary Bayesian InferenceBolstad2-1.0-29 Bolstad FunctionsBradleyTerry2-1.1-2 Bradley-Terry ModelsCATALYST-1.26.1 Cytometry dATa anALYSis ToolsCGHbase-1.62.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.2.1 Clonality Estimates in TumorCMA-1.60.0 Synthesis of microarray-based classificationCNEr-1.38.0 CNE Detection and VisualizationCOMPASS-1.40.0 Combinatorial Polyfunctionality Analysis of Single CellsCVXR-1.0-12 Disciplined Convex OptimizationCairo-1.6-2 R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) OutputCategory-2.68.0 Category AnalysisChIPpeakAnno-3.36.1 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesChIPseeker-1.38.0 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComplexHeatmap-2.18.0 Make Complex HeatmapsConsensusClusterPlus-1.66.0 ConsensusClusterPlusCytoML-2.14.0 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.25.4 Data Analysis and Graphics Data and FunctionsDECIPHER-2.30.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.56.1 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.42.1 Differential gene expression analysis based on the negative binomial distributionDEoptimR-1.1-3 Differential Evolution Optimization in Pure RDNAcopy-1.76.0 DNA Copy Number Data AnalysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.28.2 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDT-0.32 A Wrapper of the JavaScript Library ‘DataTables’DelayedArray-0.28.0 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.24.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-4.1.3 Symbolic DifferentiationDiffBind-3.12.0 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.44.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDynDoc-1.80.0 Dynamic document toolsEBImage-4.44.0 Image processing and analysis toolbox for RECOSolveR-0.5.5 Embedded Conic Solver in REpiModel-2.4.0 Mathematical Modeling of Infectious Disease DynamicsExperimentHub-2.10.0 Client to access ExperimentHub resourcesFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFNN-1.1.4 Fast Nearest Neighbor Search Algorithms and ApplicationsFlowSOM-2.10.0 Using self-organizing maps for visualization and interpretation of cytometry dataFormula-1.2-5 Extended Model FormulasGEOquery-2.70.0 Get data from NCBI Gene Expression Omnibus (GEO)GGally-2.2.1 Extension to ‘ggplot2’GO.db-3.18.0 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.28.1 GO-terms Semantic Similarity MeasuresGOstats-2.68.0 Tools for manipulating GO and microarraysGSA-1.03.2 Gene Set AnalysisGSEABase-1.64.0 Gene set enrichment data structures and methodsGSVA-1.50.1 Gene Set Variation Analysis for Microarray and RNA-Seq DataGWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association StudiesGWASTools-1.48.0 Tools for Genome Wide Association StudiesGenomeInfoDb-1.38.8 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.11 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.38.2 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.54.4 Conveniently import and query gene modelsGenomicFiles-1.38.0 Distributed computing by file or by rangeGenomicRanges-1.54.1 Representation and manipulation of genomic intervalsGetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable InterpolationGlimma-2.12.0 Interactive visualizations for gene expression analysisGlobalOptions-0.1.2 Generate Functions to Get or Set Global OptionsGmisc-3.0.3 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.34.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.46.1 Plotting data and annotation information along genomic coordinatesHDF5Array-1.30.1 HDF5 backend for DelayedArray objectsHDO.db-0.99.1 A set of annotation maps describing the entire Human Disease OntologyHMMcopy-1.44.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.22.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)HaploSim-1.8.4.2 Functions to Simulate HaplotypesHmisc-5.1-2 Harrell MiscellaneousHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIDPmisc-1.1.21 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’IHW-1.30.0 Independent Hypothesis WeightingIRanges-2.36.0 Foundation of integer range manipulation in BioconductorIRdisplay-1.1 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.30.0 Base Classes for Storing Genomic Interaction DataKEGGREST-1.42.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.62.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorLogicReg-1.6.6 Logic RegressionLymphoSeq-1.30.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-2.6.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMAST-1.28.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.35 MCMC Generalised Linear Mixed ModelsMPV-1.63 Data Sets from Montgomery, Peck and ViningMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
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ModelsRNASeqPower-1.42.0 Sample size for RNAseq studiesROCR-1.0-11 Visualizing the Performance of Scoring ClassifiersRPresto-1.4.6 DBI Connector to PrestoRProtoBuf-0.4.22 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)RProtoBufLib-2.14.1 C++ headers and static libraries of Protocol buffersRSQLite-2.3.6 SQLite Interface for RRSclient-0.7-10 Client for RserveRSpectra-0.16-1 Solvers for Large-Scale Eigenvalue and SVD ProblemsRVenn-1.1.0 Set Operations for Many SetsRaggedExperiment-1.26.0 Representation of Sparse Experiments and Assays Across SamplesRcppAnnoy-0.0.22 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
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LibraryRcppGSL-0.3.13 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppHNSW-0.6.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest
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